2013/3/6 Evren Yurtesen IB <eyurt...@abo.fi>: > Hi Christoph, > > I thought problems in the compilation is more related to devs than users. > But I sure can send mail first to users list in future. Thanks.
> > I used the following to get it working. > > mkdir build_cmake > cd build_cmake > cmake .. -DCMAKE_INSTALL_PREFIX=/export/modules/apps/gromacs/4.6.1/mvapich2 > > This does not seem to work > > mkdir build_cmake > cd build_cmake > export CMAKE_INSTALL_PREFIX=/export/modules/apps/gromacs/4.6.1/mvapich2 > cmake .. > > Was this the information you were looking for? That looks ok. I had a another look at the issue and I guess cmake's blas detention is a bit flaky, when it comes to static libraries. You are using liblapack.a, which has no link information, with liblapack.so it should have worked. Anyhow, thanks for reporting the issue. Christoph > > Thanks > Evren > > > > > On Wed, 6 Mar 2013, Christoph Junghans wrote: > >> Hi Evren, >> >> please post these kind of questions on the users list as they are not >> really related to the development of gromacs. >> >> Concerning your question below, can you please post your cmake >> configure command line? >> >> Christoph >> >> 2013/3/6 Evren Yurtesen IB <eyurt...@abo.fi>: >>> >>> Sorry for the double post. I tried to post it from web and it said the >>> post >>> was not accepted to mailing list but then it arrived anyway. >>> >>> In addition the manual mentions setting CMAKE_INSTALL_PREFIX however this >>> does not work when it is "set" it only works when given to cmake as a >>> parameter with -DCMAKE_INSTALL_PREFIX=/something >>> >>> http://www.gromacs.org/Documentation/Installation_Instructions#4.3._CMake_advanced_options >>> >>> When I do an 'export CMAKE_INSTALL_PREFIX=/something' this is does not >>> seem >>> to propagate to configuration files, interestingly 'export >>> CMAKE_PREFIX_PATH=/libpaths' seem to have the desired effect. >>> >>> Thanks, >>> Evren >>> >>> >>> On Wed, 6 Mar 2013, Evren Yurtesen IB wrote: >>> >>>> Hello, >>>> >>>> I am not exactly sure if this is a bug but I realized that cmake system >>>> of >>>> gromacs couldnt find my ATLAS libraries. First problem was that it >>>> needed >>>> -lgfortran (and then -lcblas also) for compiling with gcc. The error I >>>> found >>>> in cmake error file can be found below. >>>> >>>> In addition while documentation suggests latest GCC versions, the only >>>> compatible version of GCC with CUDA 5.0 is GCC 4.6 but there doesnt seem >>>> to >>>> be any checks for this. >>>> >>>> Run Build Command:/usr/bin/gmake "cmTryCompileExec3752895534/fast" >>>> /usr/bin/gmake -f CMakeFiles/cmTryCompileExec3752895534.dir/build.make >>>> CMakeFiles/cmTryCompileExec3752895534.dir/build >>>> gmake[1]: Entering directory >>>> `/home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp' >>>> /usr/bin/cmake -E cmake_progress_report >>>> >>>> /home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp/CMakeFiles >>>> 1 >>>> Building C object >>>> CMakeFiles/cmTryCompileExec3752895534.dir/CheckFunctionExists.c.o >>>> /export/modules/compilers/gnu/gcc/4.7.2/bin/gcc -Wextra >>>> -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused >>>> -Wunused-value -march=native -mtune=native >>>> -DCHECK_FUNCTION_EXISTS=dgemm_ >>>> -o CMakeFiles/cmTryCompileExec3752895534.dir/CheckFunctionExists.c.o >>>> -c >>>> /usr/share/cmake/Modules/CheckFunctionExists.c >>>> Linking C executable cmTryCompileExec3752895534 >>>> /usr/bin/cmake -E cmake_link_script >>>> CMakeFiles/cmTryCompileExec3752895534.dir/link.txt --verbose=1 >>>> /export/modules/compilers/gnu/gcc/4.7.2/bin/gcc -Wextra >>>> -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused >>>> -Wunused-value -march=native -mtune=native >>>> -DCHECK_FUNCTION_EXISTS=dgemm_ >>>> CMakeFiles/cmTryCompileExec3752895534.dir/CheckFunctionExists.c.o -o >>>> cmTryCompileExec3752895534 -rdynamic -Wl,-Bstatic -lf77blas -latlas >>>> -Wl,-Bdynamic >>>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/libf77blas.a(xerbla.o): In >>>> function `xerbla_': >>>> xerbla.f:(.text+0x4a): undefined reference to `_gfortran_st_write' >>>> xerbla.f:(.text+0x5a): undefined reference to >>>> `_gfortran_transfer_character_write' >>>> xerbla.f:(.text+0x6a): undefined reference to >>>> `_gfortran_transfer_integer_write' >>>> xerbla.f:(.text+0x72): undefined reference to `_gfortran_st_write_done' >>>> xerbla.f:(.text+0x7b): undefined reference to `_gfortran_stop_string' >>>> collect2: error: ld returned 1 exit status >>>> gmake[1]: *** [cmTryCompileExec3752895534] Error 1 >>>> gmake[1]: Leaving directory >>>> `/home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp' >>>> gmake: *** [cmTryCompileExec3752895534/fast] Error 2 >>>> >>>> >>>> After this the -lcblas was missing. Which caused the following errors. >>>> >>>> Run Build Command:/usr/bin/gmake "cmTryCompileExec2027137673/fast" >>>> /usr/bin/gmake -f CMakeFiles/cmTryCompileExec2027137673.dir/build.make >>>> CMakeFiles/cmTryCompileExec2027137673.dir/build >>>> gmake[1]: Entering directory >>>> `/home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp' >>>> /usr/bin/cmake -E cmake_progress_report >>>> >>>> /home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp/CMakeFiles >>>> 1 >>>> Building C object >>>> CMakeFiles/cmTryCompileExec2027137673.dir/CheckFunctionExists.c.o >>>> /export/modules/compilers/gnu/gcc/4.7.2/bin/gcc -Wextra >>>> -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused >>>> -Wunused-value -march=native -mtune=native >>>> -DCHECK_FUNCTION_EXISTS=cheev_ >>>> -o CMakeFiles/cmTryCompileExec2027137673.dir/CheckFunctionExists.c.o >>>> -c >>>> /usr/share/cmake/Modules/CheckFunctionExists.c >>>> Linking C executable cmTryCompileExec2027137673 >>>> /usr/bin/cmake -E cmake_link_script >>>> CMakeFiles/cmTryCompileExec2027137673.dir/link.txt --verbose=1 >>>> /export/modules/compilers/gnu/gcc/4.7.2/bin/gcc -Wextra >>>> -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused >>>> -Wunused-value -march=native -mtune=native >>>> -DCHECK_FUNCTION_EXISTS=cheev_ >>>> CMakeFiles/cmTryCompileExec2027137673.dir/CheckFunctionExists.c.o -o >>>> cmTryCompileExec2027137673 -rdynamic -Wl,-Bstatic -llapack -lf77blas >>>> -latlas >>>> -Wl,-Bdynamic -lgfortran >>>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarfb.o): In >>>> function `ATL_clarfb': >>>> ATL_larfb.c:(.text+0x160): undefined reference to `cblas_ccopy' >>>> ATL_larfb.c:(.text+0x1fe): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x263): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x2b9): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x400): undefined reference to `cblas_ccopy' >>>> ATL_larfb.c:(.text+0x4a4): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x509): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x55f): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x670): undefined reference to `cblas_ccopy' >>>> ATL_larfb.c:(.text+0x6f4): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x759): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x7b2): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x8b8): undefined reference to `cblas_ccopy' >>>> ATL_larfb.c:(.text+0x93f): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x9a4): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x9fd): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0xb04): undefined reference to `cblas_ccopy' >>>> ATL_larfb.c:(.text+0xb97): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0xbfd): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0xc4e): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0xd54): undefined reference to `cblas_ccopy' >>>> ATL_larfb.c:(.text+0xded): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0xe53): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0xea4): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0xf70): undefined reference to `cblas_ccopy' >>>> ATL_larfb.c:(.text+0xff8): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x105e): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x10b7): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x1180): undefined reference to `cblas_ccopy' >>>> ATL_larfb.c:(.text+0x1208): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x126e): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x12c7): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x13a7): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x140c): undefined reference to `cblas_cgemm' >>>> ATL_larfb.c:(.text+0x1464): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x14d0): undefined reference to `cblas_cgemm' >>>> ATL_larfb.c:(.text+0x1521): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x15b8): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x161d): undefined reference to `cblas_cgemm' >>>> ATL_larfb.c:(.text+0x1675): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x16e1): undefined reference to `cblas_cgemm' >>>> ATL_larfb.c:(.text+0x1732): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x17d2): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x1837): undefined reference to `cblas_cgemm' >>>> ATL_larfb.c:(.text+0x188e): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x18fb): undefined reference to `cblas_cgemm' >>>> ATL_larfb.c:(.text+0x1951): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x19eb): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x1a50): undefined reference to `cblas_cgemm' >>>> ATL_larfb.c:(.text+0x1aa7): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x1b14): undefined reference to `cblas_cgemm' >>>> ATL_larfb.c:(.text+0x1b6a): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x1bdf): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x1c78): undefined reference to `cblas_cgemm' >>>> ATL_larfb.c:(.text+0x1ccf): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x1d3c): undefined reference to `cblas_cgemm' >>>> ATL_larfb.c:(.text+0x1d95): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x1e09): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x1e8e): undefined reference to `cblas_cgemm' >>>> ATL_larfb.c:(.text+0x1ee6): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x1f4e): undefined reference to `cblas_cgemm' >>>> ATL_larfb.c:(.text+0x1fa7): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x201c): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x20b0): undefined reference to `cblas_cgemm' >>>> ATL_larfb.c:(.text+0x2108): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x2170): undefined reference to `cblas_cgemm' >>>> ATL_larfb.c:(.text+0x21c9): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x2240): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x22dc): undefined reference to `cblas_cgemm' >>>> ATL_larfb.c:(.text+0x2333): undefined reference to `cblas_ctrmm' >>>> ATL_larfb.c:(.text+0x23a0): undefined reference to `cblas_cgemm' >>>> ATL_larfb.c:(.text+0x23f9): undefined reference to `cblas_ctrmm' >>>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In >>>> function `ATL_clarft_blockFC': >>>> ATL_larft.c:(.text+0x152): undefined reference to `cblas_ctrmm' >>>> ATL_larft.c:(.text+0x1c3): undefined reference to `cblas_cgemm' >>>> ATL_larft.c:(.text+0x211): undefined reference to `cblas_ctrmm' >>>> ATL_larft.c:(.text+0x254): undefined reference to `cblas_ctrmm' >>>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In >>>> function `ATL_clarft_blockFR': >>>> ATL_larft.c:(.text+0x3bd): undefined reference to `cblas_ctrmm' >>>> ATL_larft.c:(.text+0x433): undefined reference to `cblas_cgemm' >>>> ATL_larft.c:(.text+0x481): undefined reference to `cblas_ctrmm' >>>> ATL_larft.c:(.text+0x4c4): undefined reference to `cblas_ctrmm' >>>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In >>>> function `ATL_clarft_blockBC': >>>> ATL_larft.c:(.text+0x643): undefined reference to `cblas_ctrmm' >>>> ATL_larft.c:(.text+0x69d): undefined reference to `cblas_cgemm' >>>> ATL_larft.c:(.text+0x6e8): undefined reference to `cblas_ctrmm' >>>> ATL_larft.c:(.text+0x72e): undefined reference to `cblas_ctrmm' >>>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In >>>> function `ATL_clarft_blockBR': >>>> ATL_larft.c:(.text+0x8c8): undefined reference to `cblas_ctrmm' >>>> ATL_larft.c:(.text+0x920): undefined reference to `cblas_cgemm' >>>> ATL_larft.c:(.text+0x96b): undefined reference to `cblas_ctrmm' >>>> ATL_larft.c:(.text+0x9b1): undefined reference to `cblas_ctrmm' >>>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In >>>> function `ATL_clarftFC': >>>> ATL_larft.c:(.text+0xcfb): undefined reference to `cblas_cdotc_sub' >>>> ATL_larft.c:(.text+0xdb3): undefined reference to `cblas_cdotu_sub' >>>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In >>>> function `ATL_clarftBC': >>>> ATL_larft.c:(.text+0xffd): undefined reference to `cblas_cdotc_sub' >>>> ATL_larft.c:(.text+0x10a9): undefined reference to `cblas_cdotu_sub' >>>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In >>>> function `ATL_clarftFR': >>>> ATL_larft.c:(.text+0x1368): undefined reference to `cblas_cdotc_sub' >>>> ATL_larft.c:(.text+0x1422): undefined reference to `cblas_cdotu_sub' >>>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In >>>> function `ATL_clarftBR': >>>> ATL_larft.c:(.text+0x165d): undefined reference to `cblas_cdotc_sub' >>>> ATL_larft.c:(.text+0x1713): undefined reference to `cblas_cdotu_sub' >>>> collect2: error: ld returned 1 exit status >>>> gmake[1]: *** [cmTryCompileExec2027137673] Error 1 >>>> gmake[1]: Leaving directory >>>> `/home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp' >>>> gmake: *** [cmTryCompileExec2027137673/fast] Error 2 >>>> >>>> >>>> >>>> Thanks, >>>> Evren >>>> -- >>>> gmx-developers mailing list >>>> gmx-develop...@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers >>>> Please don't post (un)subscribe requests to the list. Use the www >>>> interface or send it to gmx-developers-requ...@gromacs.org. >>>> >>> -- >>> gmx-developers mailing list >>> gmx-develop...@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-developers >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface >>> or send it to gmx-developers-requ...@gromacs.org. >> >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> > -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
